AMBER Archive (2006)

Subject: Re: AMBER: MM-PBSA

From: Angelo (angelo_at_holmes.cancres.nottingham.ac.uk)
Date: Mon Dec 18 2006 - 10:30:00 CST

Hi,

I think that it depends from your simulation, first of all you should
check the equilibration of your simulation ( plotting RMSD, EAMBER, etc.
etc). Let's say that your 10 ns simulation shows a constant RMSD after 3
ns...after this point you may want to start your MM-PBSA analysys. You
can check the Standard Deviation of your analysys, if considering only
the last 2 ns of the simulation the SD is considerably smaller than
considering the last 8 ns, then the former is probably the best choice.

I think that there is no preferred method, you should choose the
protocol which better suite your situation and to know that you should
try more than one thing...curiosity is the basis of research.

I hope that somebody more expert than me can add something here.

regards

Angelo

Shozeb Haider wrote:

> Hi
>
> I am trying to perform MM-PBSA calculations on an MD run (10ns). I
> have been reading several protocols and I was wondering about 2 things.
>
> 1. How would my calculations differ if I take snapshots every 250ps
> over the last 8ns instead of snapshots taken at 10ps interval during
> the last 2ns of my simulations ?
>
> 2. Why is latter the preferred method ?
>
> I shall extremely grateful to make me understand this point.
>
> Best wishes
>
> Shozeb Haider
> The London School of Pharmacy
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